I just have one comment on the multi-language support in R Markdown (inline below):
On Thu, Oct 11, 2018 at 6:19 AM Ista Zahn <istaz...@gmail.com> wrote: > > Hi Spencer, > > On Thu, Oct 11, 2018 at 5:08 AM Spencer Graves > <spencer.gra...@effectivedefense.org> wrote: > > > > Hello: > > > > > > What are the differences between Jupyter notebooks and RMarkdown > > vignettes? > > Here are some of the main differences I'm aware of: > > Rmarkdown files include code and prose. The results produced by the > code do not appear in the Rmarkdown file; instead, the file must be > processed and typeset to produce a .pdf or .html (etc.) file that > includes those results. Jupyter notebooks dispense with with > processing step: output is displayed directly in the notebook. That > is, a notebook includes code, prose, and results, while an Rmarkdown > file includes only code and prose. > > Rmarkdown allows control over the inclusion of code and results, and > over how the results are displayed via header arguments. There is no > such thing in Jupyter notebooks. Controlling the precise appearance of > a document produced by Jupyter is much more difficult. Going farther, > one can even say that Jupyter notebooks are designed primarily to be > read as Jupyter notebooks; exporting to other formats is kind of an > afterthought. In contrast, Rmarkdown is designed to produce the final > readable result in another format (.html or .pdf typically). > > Rmarkdown is based on markdown, a human readable markup language, > Jupyter notebooks are based on JSON, a data interchange format common > on the web. This means that Rmarkdown files can be easily edited using > any text editor you like. The same is not true of Jupyter notebooks. > While you can of course edit the JSON directly, the format is designed > to be written and read by a computer; editing it yourself is not easy. > > Rmarkdown is specific to R (I guess there is some basic support in > knitr for other languages, but in my experience it never worked well) > while Jupyter notebooks are language agnostic and "kernels" exist for > a large number of programming languages. However, each Jupyter > notebook can use only one kernel; you can't easily have R and Python > code in the same notebook. You might want to at least update your impression about the Python support in R Markdown now :) Last year, with the release of the reticulate package, the support for Python has been substantially enhanced in both R Markdown (https://bookdown.org/yihui/rmarkdown/language-engines.html) and RStudio (https://blog.rstudio.com/2018/10/09/rstudio-1-2-preview-reticulated-python/). You can easily have both R and Python code in the same R Markdown document, and the two worlds can freely talk to each other. > Jupyter notebooks typically run in your browser where the actual text > editing features are somewhat limited. Rmarkdown is typically run in > an editor such as Emacs or Rstudio where editing and project support > is much better and greater customization may be possible. You can work > indirectly with Jupyter notebooks in Emacs > (https://github.com/millejoh/emacs-ipython-notebook) and perhaps other > editors as well; this goes some way toward escaping the tyranny of the > browser but is more fragile and difficult to get working compared to > Rmarkdown. > > Because Jupyter uses a web-based client-server model, it is easy to > provide live interactive notebooks on your website (see e.g., > https://github.com/jupyterhub/binderhub). As far as I know this is not > currently possible with Rmarkdown. > > > > > > > I'm trying to do real time monitoring of the broadcast quality of > > a radio station, and it seems to me that it may be easier to do that in > > Python than in R.[1] This led me to a recent post to > > "python-l...@python.org" that mentioned "Jupyter, Mathematica, and the > > Future of the Research Paper"[2] by Paul Romer, who won the 2018 Nobel > > Memorial Prize in Economics only a few days ago. In brief, this article > > suggests that Jupyter notebooks may replace publication in refereed > > scientific journals as the primary vehicle for sharing scientific > > research, because they make it so easy for readers to follow both the > > scientific and computational logic and test their own modifications. > > > > > > A "Jupyter Notebook Tutorial: The Definitive Guide"[3] suggested > > I first install Anaconda Navigator. I got version 1.9.2 of that. It > > opens with options for eight different "applications" including > > JupyterLab 0.34.9, Jupyter Notebook 5.6.0, Spyder 3.3.1 (an IDE for > > Python), and RStudio 1.1.456. > > > > > > This leads to several questions: > > > > > > 1. In general, what experiences have people had with > > Jupyter Notebooks, Anaconda Navigator, and RMarkdown vignettes in > > RStudio, and the similarities and differences? Do you know any > > references that discuss this? > > I've used both extensively, and noted the differences I've discovered above. > > > > > > > 2. More specifically, does it make sense to try to use > > RStudio from within Anaconda Navigator, or is one better off using > > RStudio as a separate, stand alone application -- or should one even > > abandon RStudio and run R instead from within a Jupyter Notebook? [I'm > > new to this topic, so it's possible that this question doesn't even make > > sense.] > > The only advantage I can think of to using Rstudio via Anaconda is > that you could use conda environments to maintain different versions > or R and/or R packages for different projects. > > You'll have to weigh the pros and cons to decide whether to switch > from Rstudio to Jupyter notebooks. Depending on what you want to do > there are both advantages and disadvantages, as discussed above. > > Finally, I have to give a plug for a couple of related tools that I > find very useful. > > Emacs org-mode https://orgmode.org/ gives you the best of both worlds: > notebooks unconstrained by the browser that can include code in > multiple languages, header arguments, excellent export support, etc. > It is superior to both Jupyter and Rmarkdown, except that support only > exists in Emacs. > > Jupytext (https://github.com/mwouts/jupytext) is another way to have > it all, by allowing you to edit in markdown or Rmarkdown, and > auto-generating a notebook and possibly other formats for you. I've > only recently started experimenting with it, but so far I like it a > lot. > > Best, > Ista > > > > > > Thanks, > > Spencer Graves > > > > > > [1] If you have ideas for how best to do real time monitoring of > > broadcast quality of a radio station, I'd love to hear them. I need > > software that will do that, preferably something that's free, open > > source. The commercial software I've seen for this is not adequate for > > my purposes, so I'm trying to write my own. I have a sample script in > > Python that will read a live stream from a radio tuner and output a > > *.wav of whatever length I want, and I wrote Python eight years ago for > > a similar real time application. I'd prefer to use R, but I don't know > > how to get started. > > > > > > [2] 2018-04-13: > > "https://paulromer.net/jupyter-mathematica-and-the-future-of-the-research-paper";. > > This further cites a similar article in The Atlantic from 2018-04-05: > > "www.theatlantic.com/science/archive/2018/04/the-scientific-paper-is-obsolete/556676". ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
